In Life Cycle Impact Assessment (LCIA) both spatial variability and model choices may be influential. In the case of the effect model, the effect factors differ with respect to their assumption of linear/nonlinear responses to increases in environmental stressor levels, and whether or not they account for the current stressor levels in the environment. Here, we derived spatially explicit characterization factors of phosphorus emissions causing eutrophication based on three different effect models (depicted by marginal, linear, and average effect factors) and two freshwater types (lakes and streams) and we performed an analysis of variance (ANOVA) to investigate how the selection of the effect models and the freshwater types influence the impacts of phosphorus emissions to freshwater on heterotrophic species. We found that 56% of the variability of ecological impacts per unit of phosphorus emission was explained, primarily, by the difference between freshwater types and, to a lesser extent, by the difference between effect models. The remaining variability was attributed to the spatial variation between river basins, mainly due to the variability in fate factors. Our study demonstrates the particular importance of accounting for spatial variability and model choices in LCIA.